Genome-wide DNA methylation analysis of pulmonary function in middle and old-aged Chinese monozygotic twins

Background Previous studies have determined the epigenetic association between DNA methylation and pulmonary function among various ethnics, whereas this association is largely unknown in Chinese adults. Thus, we aimed to explore epigenetic relationships between genome-wide DNA methylation levels and pulmonary function among middle-aged Chinese monozygotic twins. Methods The monozygotic twin sample was drawn from the Qingdao Twin Registry. Pulmonary function was measured by three parameters including forced expiratory volume the first second (FEV1), forced vital capacity (FVC), and FEV1/FVC ratio. Linear mixed effect model was used to regress the methylation level of CpG sites on pulmonary function. After that, we applied Genomic Regions Enrichment of Annotations Tool (GREAT) to predict the genomic regions enrichment, and used comb-p python library to detect differentially methylated regions (DMRs). Gene expression analysis was conducted to validate the results of differentially methylated analyses. Results We identified 112 CpG sites with the level of P < 1 x 10(-4) which were annotated to 40 genes. We identified 12 common enriched pathways of three pulmonary function parameters. We detected 39 DMRs located at 23 genes, of which PRDM1 was related to decreased pulmonary function, and MPL, LTB4R2, and EPHB3 were related to increased pulmonary function. The gene expression analyses validated DIP2C, ASB2, SLC6A5, and GAS6 related to decreased pulmonary function. Conclusion Our DNA methylation sequencing analysis on identical twins provides new references for the epigenetic regulation on pulmonary function. Several CpG sites, genes, biological pathways and DMRs are considered as possible crucial to pulmonary function.Peer reviewe

Genome-wide DNA methylation and gene expression analyses in monozygotic twins identify potential biomarkers of depression

Depression is currently the leading cause of disability around the world. We conducted an epigenome-wide association study (EWAS) in a sample of 58 depression score-discordant monozygotic twin pairs, aiming to detect specific epigenetic variants potentially related to depression and further integrate with gene expression profile data. Association between the methylation level of each CpG site and depression score was tested by applying a linear mixed effect model. Weighted gene co-expression network analysis (WGCNA) was performed for gene expression data. The association of DNA methylation levels of 66 CpG sites with depression score reached the level of P < 1 x 10(-4). These top CpG sites were located at 34 genes, especially PTPRN2, HES5, GATA2, PRDM7, and KCNIP1. Many ontology enrichments were highlighted, including Notch signaling pathway, Huntington disease, p53 pathway by glucose deprivation, hedgehog signaling pathway, DNA binding, and nucleic acid metabolic process. We detected 19 differentially methylated regions (DMRs), some of which were located at GRIK2, DGKA, and NIPA2. While integrating with gene expression data, HELZ2, PTPRN2, GATA2, and ZNF624 were differentially expressed. In WGCNA, one specific module was positively correlated with depression score (r = 0.62, P = 0.002). Some common genes (including BMP2, PRDM7, KCNIP1, and GRIK2) and enrichment terms (including complement and coagulation cascades pathway, DNA binding, neuron fate specification, glial cell differentiation, and thyroid gland development) were both identified in methylation analysis and WGCNA. Our study identifies specific epigenetic variations which are significantly involved in regions, functional genes, biological function, and pathways that mediate depression disorder.Peer reviewe

Genetic and Environmental Influences on Cardiovascular Disease Risk Factors : A Study of Chinese Twin Children and Adolescents

Peer reviewe

A multiple-antigen detection assay for tuberculosis diagnosis based on broadly reactive polyclonal antibodies

Objective(s): Detection of circulating Mycobacterium tuberculosis (M. tuberculosis) antigens is promising in Tuberculosis (TB) diagnosis. However, not a single antigen marker has been found to be widely expressed in all TB patients. This study is aimed to prepare broadly reactive polyclonal antibodies targeting multiple antigen markers (multi-target antibodies) and evaluate their efficacies in TB diagnosis. Materials and Methods: A fusion gene consisting of 38kD, ESAT6, and CFP10 was constructed and overexpressed. The fusion polyprotein was used as an immunogen to elicit production of multi-target antibodies. Their reactivities were tested. Then, the multi-target antibodies and three corresponding antibodies elicited by each single antigen (mono-target antibodies) were evaluated with sandwich ELISA for detecting M. tuberculosis antigens. Their diagnostic efficacies for TB were also compared. Results: The polyprotein successfully elicited production of multi-target antibodies targeting 38kD, ESAT6, and CFP10 as analyzed by Western blotting. When used as coating antibodies, the multi-target antibodies were more efficient in capturing the three antigens than the corresponding mono-target antibodies. By testing clinical serum, the multi-target antibodies demonstrated significantly higher sensitivity for clinical TB diagnosis than all three mono-target antibodies. Conclusion: The multi-target antibodies allowed detecting multiple antigens simultaneously and significantly enhanced TB detection compared to routine mono-target antibodies. Our study may provide a promising strategy for TB diagnosis

A de novo Genome of a Chinese Radish Cultivar

AbstractHere, we report a high-quality draft genome of a Chinese radish (Raphanus sativus) cultivar. This draft contains 387.73Mb of assembled scaffolds, 83.93% of the scaffolds were anchored onto nine pseudochromosomes and 95.09% of 43 240 protein-coding genes were functionally annotated. 184.75Mb (47.65%) of repeat sequences was identified in the assembled genome. By comparative analyses of the radish genome against 10 other plant genomes, 2 275 genes in 780 gene families were found unique to R. sativus. This genome is a good reference for genomic study and of great value for genetic improvement of radish